I think the project you're working on has great potential if done right!
- Personally, seeing as youre using Citizens, i would look into a citizens add-on called Denizen, and one called DTLTraders. DTLTraders is a shopping store plugin, made entirely through NPC's, its really usefull! Denizen is a API that enables you to do quests, chat dialogues and stuff like that with NPC's. I could see that as being good additions to your project. You could come up with some intresting lore that way =)
Also, when you build the cities, i highly suggest building normal modern cities across the map, have them look all nice at the start, then use a tool as WorldEdit, to brush air over it. You would do that with doing //brush sphere 5 0 (5 radious, 0 for air), then you click the buildings everywhere etc, to give them holes and stuff, thatll make it look like ruins. Its possibly the best and easiest way to make buildings look like ruins, while still having them look nice. In theory, you could look around for modern cities here on PMC, ask the owners of them, if you can use them for inspiration, and then tear em up! Thats the quickest way you can do this =)
To make some awesome custom terrain, i would look into the WGEN program called WorldPainter. Its really fancy, and extremely good for making custom terrain!
If you wish to give the project a more "survival apocalyptic" feel, you could also look into SpoutPlugin, API+ and Guns+. Thatll enable you to add guns to the game, that can be fired.
VariableTriggers is a plugin that you could use aswell. It enables you to make "events" in regions that YOU define. That means you could make a house, have 10 zombies spawn when you enter it, and when the zombies are killed, a treasure chest with goods would spawn. Once you leave the building, it would reset.
Thats the ideas i have on top of my head =) I hope to see this succeed! Could be quite intresting. Good luck buddy!